Problem extracting features from convolutional layer where the dimensions are big for feature maps
I think it's okay to let CNN extract a big number of feature maps, then you can reduce the features from it. To reduce features from CNN result, you can do feature selection or feature extraction. Some people prefer to use feature selection and select the most significant feature maps, for examples:


Action unit selective feature maps in deep networks for facial expression recognition
Convolutional Neural Network Simplification Based on Feature Maps Selection


Hope it helps.